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biopet.biopet
Commits
7439f3d4
Commit
7439f3d4
authored
Nov 17, 2014
by
Peter van 't Hof
Browse files
Fix typo
parent
fe78d034
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
7439f3d4
...
...
@@ -61,12 +61,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if
(
files
.
size
==
1
)
return
files
if
(
files
.
isEmpty
)
throw
new
IllegalStateException
(
"Files can't be empty"
)
if
(!
doublePreProces
.
get
)
return
files
val
markDu
b
=
MarkDuplicates
(
this
,
files
,
new
File
(
outputDir
+
outputName
+
".dedup.bam"
))
add
(
markDu
b
,
isIntermediate
=
useIndelRealigner
)
val
markDu
p
=
MarkDuplicates
(
this
,
files
,
new
File
(
outputDir
+
outputName
+
".dedup.bam"
))
add
(
markDu
p
,
isIntermediate
=
useIndelRealigner
)
if
(
useIndelRealigner
)
{
List
(
addIndelRealign
(
markDu
b
.
output
,
outputDir
,
isIntermediate
=
false
))
List
(
addIndelRealign
(
markDu
p
.
output
,
outputDir
,
isIntermediate
=
false
))
}
else
{
List
(
markDu
b
.
output
)
List
(
markDu
p
.
output
)
}
}
...
...
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